[chimera-dev] Save PDB and Map before fitting

[Pablo Solar Rodríguez]

Hello Eric,

Thank you for the response. I will check it!!

Kind regards!

2017-04-26 19:28 GMT+02:00 Eric Pettersen <pett at cgl.ucsf.edu>:

> Hi Pablo,
> Every model has an ‘openState’ attribute which in turn has a ‘xform’
> attribute which holds the model’s transformation matrix.  A newly opened
> model, if it’s the only model, will have the identity matrix as it’s
> initial xform.  If there are other models open, then its initial xform will
> be the same as that of the currently open model with the lowest ID number,
> in a “best effort” attempt to keep the newly opened model in the same frame
> of reference as the other models.
> So to see if you need to resave it you should compare the current xform to
> the one it had the last time you saved it.
> There is a trigger that fires when a model’s transformation matrix changes
> — the ‘OpenState’ trigger will fire in the chimera.triggers trigger set,
> with the trigger data ‘.reasons’ attribute containing ‘transformation
> change’.  However, there is a convenience trigger, chimera.MOTION_STOP,
> that you probably want to register for instead, that will collate all the
> many OpenState trigger firings that will occur during a mouse motion.  That
> trigger is also in the chimera.triggers trigger set.  If you aren’t
> familiar with triggers, there is a programmer example about them:
>
> https://www.cgl.ucsf.edu/chimera/current/docs/ProgrammersGuide/Examples/
> Main_AtomTrigger.html
>
> —Eric
>
>
> Eric Pettersen
> UCSF Computer Graphics Lab
>
>
> On Apr 26, 2017, at 12:41 AM, Pablo Solar Rodríguez <
> pablo.solar at delogica.com> wrote:
>
>
> Hello Elaine,
>
> Thank you for the quick response. I'll check the info to find a way to do
> it. Just one more thing. Is there a manner to know when the map has been
> moved? Just to not resampling it each time needlessly.
>
> Thank you!
>
>
>
> El 25-04-2017 18:21, Elaine Meng escribió:
>
> Hi Pablo,
> The map format doesn't include rotation information.  You would have to
> resample it on a new grid to create a new map, such as with command "vop
> resample"... details here on saving maps after fitting (bottom of the page):
>
> <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/
> savemodel.html#afterfitting>
>
> I hope this helps,
> Elaine
> ----------
> Elaine C. Meng, Ph.D.
> UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab
> Department of Pharmaceutical Chemistry
> University of California, San Francisco
>
> On Apr 25, 2017, at 2:24 AM, Pablo Solar Rodríguez <
> pablo.solar at delogica.com> wrote:
>
> Hello Tom,
> Thank you for your quick response. I've checked the code in my plugin and
> the PDB saving works fine as I expected, even if I move the molecule.
>
> My question is about saving the map. I tried to move it (rotate&translate
> unchecking the 'A' in the ModelPanel) and then save it with this code, but
> when I open the saved map, it is similar to the original one and does not
> keep the new coordinates. This could be a problem in my plugin, because I
> need to save them case of moving to get correct results in the fitting
> process.
>
> So, how can I handle this situation? Is there any other way for saving the
> new map coordinates in the same way the PDB saving does? Hope I have
> explained myself correctly.
> Thank you in advance and kind regards,
> Pablo.
>
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-- 

*Pablo Solar Rodríguez*

*pablosolar.r at gmail.com <pablosolar.r at gmail.com>*
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